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View Code? Open in Web Editor NEWA vocabulary for describing Zebrafish Phenotypes
Home Page: https://obophenotype.github.io/zebrafish-phenotype-ontology/
A vocabulary for describing Zebrafish Phenotypes
Home Page: https://obophenotype.github.io/zebrafish-phenotype-ontology/
Apart from phenotypic abnormalities, ZFIN curates ameliorated and excacerbated phenotypes. These phenotypes are special in two senses
Now the problem is that (1) adding those into ZP will lead to two large branches with 3000 - 9000 terms being added (term proliferation), and (2) there is no integration between the two, or, indeed with anything in uPheno.
My sense is the ship to prevent term proliferation has sailed. We should just add these phenotypes the same way as the we have the others.
However, I do think we should move uPheno to the "changed" qualifier throughout so that we can group ameliorated, exacerbated and abnormal in a more general "phenotype" hierarchy.
There are currently a few duplicate classes in ZP that need to go.
Advantages
Problems to overcome
When we don't have a term, we need to rapidly create new terms.
When running ZFIN pipeline, I only ever see classes added, not anything removed. This is a note to self and does not require action for now.
We have the following 18 missing GO terms needed to construct a total of 44 classes in ZP. Most likely these classes were, at some point in the past, used by ZFIN to describe phenotypes. We need to decide what to do with these.
@ybradford while I am preparing a new release, can you determine what happened with these and if they are still needed by ZFIN? I could just mass obsolete all phenotypes related to these classes, but it seems unfortunate to keep obsoleting so many classes per year.
(a) what happened with these (some don't resolve in GO)
http://amigo.geneontology.org/amigo/term/GO:0044420
http://amigo.geneontology.org/amigo/term/GO:0044424
These are the corresponding annotations:
ZDB-FISH-180927-4 olfm1a<sup>sa221/sa221</sup> ; olfm1b<sup>sa157/sa157</sup>(TL) ZDB-STAGE-010723-32 Pharyngula:Prim-15 ZDB-STAGE-010723-32 Pharyngula:Prim-15 GO:0044424 obsolete intracellular part BFO:0000050 part_of ZFA:0000152 retina PATO:0001997 decreased amount abnormal ZDB-PUB-171005-5 ZDB-EXP-180927-1 GO:0044424-BFO:0000050-ZFA:0000152-PATO:0001997-0-0-0 ZP:0110355
ZDB-FISH-150901-2115 gpc4<sup>m119/m119</sup> ZDB-STAGE-010723-36 Larval:Day 5 ZDB-STAGE-010723-36 Larval:Day 5 GO:0044420 obsolete extracellular matrix component BFO:0000050 part_of ZFA:0001458 cranial cartilage PATO:0000060 spatial pattern normal ZDB-PUB-110518-25 ZDB-EXP-041102-1 GO:0044420-BFO:0000050-ZFA:0001458-PATO:0000060-0-0-0 ZP:0110354
ZDB-FISH-150901-24314 ext2<sup>to273b/to273b</sup> ZDB-STAGE-010723-36 Larval:Day 5 ZDB-STAGE-010723-36 Larval:Day 5 GO:0044420 obsolete extracellular matrix component BFO:0000050 part_of ZFA:0001458 cranial cartilage PATO:0000060 spatial pattern abnormal ZDB-PUB-110518-25 ZDB-EXP-041102-1 GO:0044420-BFO:0000050-ZFA:0001458-PATO:0000060-0-0-0 ZP:0110354
ZDB-FISH-150901-2448 slc35b2<sup>to216z/to216z</sup> ZDB-STAGE-010723-36 Larval:Day 5 ZDB-STAGE-010723-36 Larval:Day 5 GO:0044420 obsolete extracellular matrix component BFO:0000050 part_of ZFA:0001458 cranial cartilage PATO:0000060 spatial pattern abnormal ZDB-PUB-110518-25 ZDB-EXP-041102-1 GO:0044420-BFO:0000050-ZFA:0001458-PATO:0000060-0-0-0 ZP:0110354
ZDB-FISH-150901-28521 b3gat3<sup>hi307Tg/hi307Tg</sup> ZDB-STAGE-010723-36 Larval:Day 5 ZDB-STAGE-010723-36 Larval:Day 5 GO:0044420 obsolete extracellular matrix component BFO:0000050 part_of ZFA:0001458 cranial cartilage PATO:0000060 spatial pattern normal ZDB-PUB-110518-25 ZDB-EXP-041102-1 GO:0044420-BFO:0000050-ZFA:0001458-PATO:0000060-0-0-0 ZP:0110354
ZDB-FISH-150901-29430 uxs1<sup>hi954Tg/hi954Tg</sup> ZDB-STAGE-010723-36 Larval:Day 5 ZDB-STAGE-010723-36 Larval:Day 5 GO:0044420 obsolete extracellular matrix component BFO:0000050 part_of ZFA:0001458 cranial cartilage PATO:0000060 spatial pattern abnormal ZDB-PUB-110518-25 ZDB-EXP-041102-1 GO:0044420-BFO:0000050-ZFA:0001458-PATO:0000060-0-0-0 ZP:0110354
Output should be a table with
ZP, ZFIN EQ ID, OBSOLETE CLASS
ZP:001,0-0-0-PATO:001-0-0-0,GO:0001
Currently will need to make use of existing annotations to establish the link. Other ideas?
ZFIN is using the following obsolete GO term in annotation:
ZDB-FISH-170818-7 TU + MO2-bptf + MO3-bptf ZDB-STAGE-010723-18 Gastrula:75%-epiboly ZDB-STAGE-010723-18 Gastrula:75%-epiboly GO:0016584 obsolete nucleosome positioning PATO:0001236 process quality abnormal ZDB-PUB-150605-3 ZDB-EXP-070511-5 0-0-GO:0016584-PATO:0001236-abnormal-0-0-0
Obsolete GO term in ZFIN:
ZDB-FISH-170831-28 WT + MO1-tyrp1a + MO2-tyrp1b ZDB-STAGE-010723-9 Hatching:Long-pec ZDB-STAGE-010723-9 Hatching:Long-pec GO:0048876 obsolete chemical homeostasis within retina BFO:0000066 occurs_in ZFA:0000144 retinal pigmented epithelium PATO:0001507 disrupted abnormal ZDB-PUB-160505-5 ZDB-EXP-041102-1 GO:0048876-BFO:0000066-ZFA:0000144-PATO:0001507-abnormal-0-0-0
The definition currently is (coming from ZFIN EQs):
'has part' some
(absent and ('inheres in' some
('intersegmental vessel' and ('part of' some 'thoracic duct'))) and ('has modifier' some abnormal))
The problem is this:
lymphatic vessel is disjoint with blood vessel.
However, the bearer above (('intersegmental vessel' and ('part of' some 'thoracic duct'))
) is both a blood vessel (an intersegmental vessel is a blood vessel according to ZFA) AND a lymphatic vessel:
lymph vasculature
, becausethoracic duct
is a lymphatic vessel and 3.2.
thoracic ductis part of the
lymph vasculature`.I dont know anatomy well enough to fix this, but @ybradford maybe you can see how to fix.
See attached file:
zp_zfin_phenotype_fish_go_plus_quality.txt
Not all of them will be wrong (when GO cellular components are used); maybe we can cut some of them down. But most of them are.
Hi. My understanding from ZFIN is that they won't integrate with NBO but are staying with the levels of behavioural process provided by integrating with GO. If so, I am puzzled to find a single example of an NBO term (and its parents) in the ZP ontology: ‘chewing’ (NBO:0000073). I wonder why, not least because the ZP ontology also contains its synonym 'mastication' (GO:0071626).
@matentzn commented on Tue Sep 25 2018
For example, 'abnormally abnormal angiogenic sprout' (ZP_0003681) in the last main build refers to the quality 'abnormal' (PATO:0000460). In the current ZFIN metadata (neither gene nor genome data), there is no single annotation that refers to both the angiogenic sprout (ZFA:0005604) and the PATO quality 'abnormal'.
@drseb is that possible?
@matentzn commented on Tue Sep 25 2018
In the case that a phenotype that previously existed now changed, we should obsolete the existing class (remove the definition) but still add it to the new ontology.
@drseb commented on Tue Sep 25 2018
Can you help debug? Which gene/genotype/morpholino has previously been associated with that?
@matentzn commented on Tue Sep 25 2018
I looked through the old versions of the old ZFIN raw data. There are many annotations with the sprout, but none that have the abnormal Qualifier in the place of the Quality. I gladly keep looking at this issue, but my expectation is that such changes can and will occur from time to time..
@drseb commented on Tue Sep 25 2018
Yes. Those issues will arise often. Hmm... we need a new strategy. Obsoletion is probably not solving the issue, because what will happen if it is used in a future release? Unobsolete again?
@matentzn commented on Tue Sep 25 2018
That is what I was thinking! Why not :P
@drseb commented on Tue Sep 25 2018
If you think it is a valid option I am okay with it. Would love to hear from others if that is okay. @balhoff ?
@matentzn commented on Tue Sep 25 2018
I mean, there are three alternatives:
Both 2 and 3 are valid, as a phenotypic description does not necessarily become invalid just because it is not used in any of the annotations. Above case is a bit of an exception, because I am trying to push the community to distinguish between modifiers and qualities, and abnormal is not a quality, it is a modifier, and therefore does not belong in the quality slot. I advocate 2. I dont think 1. is a good option at all, both for administrative and conceptual reasons.
@matentzn commented on Tue Sep 25 2018
@dosumis @cmungall if you have strong opinions here
@drseb commented on Tue Sep 25 2018
At the moment (I have to think about it again later) I vote for 3, as it is the simplest solution.
But this would require more information about the reason for the class' disappearance in the ZFIN data. Can we get a comment from ZFIN on typical reasons? If they simply replaced it with a more specific annotation, then the previously chosen class is still correct. If it was a clear error in the first place than option 2 would be the better choice. Let's hear what others say ;-)
@matentzn commented on Tue Sep 25 2018
I pinged them on slack. :)
@matentzn commented on Tue Sep 25 2018
I quickly took a look at the diffs:
As an irrelevant side note: I also noticed that 105 labels (from all those phenotypes that appear in both versions of ZP) vary quite significantly (either because labels in GO change, or in PATO, or perhaps in ZFA).
@balhoff commented on Tue Sep 25 2018
I'm okay with "un-obsoleting" when needed. However I feel like if the expression is satisfiable, it doesn't hurt anything to keep in (option 3). Some others outside of ZFIN are using ZP (for example Rong-Lin).
@drseb commented on Wed Sep 26 2018
@cmungall this is all so long ago... (we were so young back then ;-) ). Do you remember more details from our work? It is not written in the F1000 paper, but looking at the classes that have no direct gene association I assume that we automatically generated more general class expressions. E.g. abnormal length X would imply that we add abnormal X to ZP. (I think we have done this, but I am not sure)
These will not be logically defined (but maybe partially)
@ybradford to gather one or more examples with human readable definition that we can work on together.
By far the majority will not be root unsatisfiable; I need to run some experiments and see which ones are broken ones (probably only a handful using part of instead of occurs in), and submit them to ZFIN to be fixed.
is:
'has part' some quality
should be:
'has part' some (quality and inheres in some owl:Thing and 'has modifier' some abnormal)
ZFIN annotations are not free of redundancy. For example, we occasionally have annotations to somite
, and on other cases somite and part of trunk
. Unfortunately, somite
is ALWAYS part of trunk (ZFA). The problem is, since we rely on the annotations to be logically distinct, we generate both classes: inheres in somite
, and inheres in somite part of trunk
, which are logically equivalent and therefore redundant and confusing. For ZP, as a workaround, we remove part of axioms from ZFA prior to generating the ontology. But that wont really help us, when ZP is combined with other ontologies.
Do you think it makes sense to fix these annotations at ZFIN @ybradford annotations;
Logical definition:
'has part' some
('process quality' and ('inheres in' some
('glutathione transferase activity' and ('part of' some 'whole organism')))
Problem: 'glutathione transferase activity' is a process, 'whole organism' a material entity. part_of is the wrong relation.
Solution: ZFIN record should use 'occurs_in' in column Post-composed Relationship ID
instead of 'part_of'. Note that this entry comes from a 'normal' phenotype entry; it should nevertheless be correct.
Refer to this table to find the broken record.
For new term requests, please provide the following information:
abnormal tail morphology
combination of UBERON tail and PATO malformed
not sure
If you would like a nanoattribution, please indicate your ORCID id
ZFIN references ZFA:0005943, but I cannot find it in ZFA at all.. @ybradford can you track this term down?
Not on OLS, nor on Ontobee, e.g. https://www.ebi.ac.uk/ols/search?q=ZFA%3A0005943&groupField=iri&exact=on&start=0
ZDB-FISH-150901-15216 TU ZDB-STAGE-010723-10 Pharyngula:Prim-5 ZDB-STAGE-010723-10 Pharyngula:Prim-5 GO:0006508 proteolysis BFO:0000066 occurs_in ZFA:0005943 perivitelline fluid PATO:0002304 increased process quality abnormal ZDB-PUB-200207-23 ZDB-EXP-210520-3 GO:0006508-BFO:0000066-ZFA:0005943-PATO:0002304-abnormal-0-0-0
ZDB-FISH-150901-15216 TU ZDB-STAGE-010723-13 Pharyngula:Prim-25 ZDB-STAGE-010723-13 Pharyngula:Prim-25 GO:0006508 proteolysis BFO:0000066 occurs_in ZFA:0005943 perivitelline fluid PATO:0002304 increased process quality abnormal ZDB-PUB-200207-23 ZDB-EXP-210520-3 GO:0006508-BFO:0000066-ZFA:0005943-PATO:0002304-abnormal-0-0-0
It appears that all the following classes follow the same problem: a kind of activity occurs in an anatomy, but ZFIN uses 'part_of' instead of 'occurs_in' to model this. So I guess our unsatisfiable problem is smaller than I thought.
Phenotypes with activities that occur in an anatomical structure:
Laminase binding
Example:
'has part' some
('increased occurrence' and ('inheres in' some
('protein kinase activity' and ('part of' some 'cardiac ventricle')))
and ('has modifier' some abnormal))
Problem: 'protein kinase activity' is a process, cardiac ventrical a material entity. part_of is the wrong relation.
Solution: ZFIN record should use 'occurs_in' in column Post-composed Relationship ID
instead of 'part_of'.
Refer to this table to find the broken record.
If the record is not found in the above table, it means that the culprit lies in one of the intermediate classes we have already added; just post here which ones and I will fix them.
Example:
ZDB-FISH-150901-29105 WT ZDB-STAGE-010723-8 Larval:Protruding-mouth ZDB-STAGE-010723-8 Larval:Protruding-mouth ZFA:0001315 atrioventricular canal PATO:0002001 has fewer parts of type abnormal GO:0005623 cell BFO:0000050 part_of ZFA:0001320 endocardium ZDB-PUB-130709-36 ZDB-EXP-140306-9 0-0-ZFA:0001315-PATO:0002001-GO:0005623-BFO:0000050-ZFA:0001320 ZP:0014564
Compared to:
ZDB-FISH-150901-24930 gdf6a<sup>m233/m233</sup>(AB) ZDB-STAGE-010723-35 Larval:Day 4 ZDB-STAGE-010723-35 Larval:Day 4 ZFA:0009000 cell BFO:0000050 part_of ZFA:0000119 retinal inner nuclear layer PATO:0001997 decreased amount abnormal ZDB-PUB-101115-22 ZDB-EXP-041102-1 ZFA:0009000-BFO:0000050-ZFA:0000119-PATO:0001997-0-0-0 ZP:0006134
This causes confusion for the labels: both classes GO:0005623 and ZFA:0009000 are labelled 'cell'. Intentional?
ZP:0008499
ZP:0000998
These two phenotypes have the same label, but are defined differently. @ybradford in our next face 2 face, we can look at this one.
@ybradford ZFIN is using the following obsolete GO term:
ZDB-FISH-151223-12 esco2<sup>hi2865Tg/hi2865Tg</sup> ZDB-STAGE-010723-10 Pharyngula:Prim-5 ZDB-STAGE-010723-10 Pharyngula:Prim-5 GO:0007083 obsolete mitotic chromosome decondensation PATO:0000694 premature abnormal ZDB-PUB-150606-7 ZDB-EXP-041102-1 0-0-GO:0007083-PATO:0000694-abnormal-0-0-0
@matentzn commented on Mon Sep 10 2018
In 'Phenotype of Zebrafish Genes' dataset (https://zfin.org/downloads/phenoGeneCleanData_fish.txt), ZFIN annotates a few genes using BSPO:0000120 (in left side of) and the respective 'in right side of'. Both BSPO identifiers refer to object properties, not classes; ZPGen assumes the column contains classes. Question to @ybradford : These are only a handful of records; is it possible that the intention was to use BSPO:0000000
(left side) or BSPO:0000007
(right side) instead?
/data $ wget https://zfin.org/downloads/phenoGeneCleanData_fish.txt
/data $ grep BSPO:0000120 phenoGeneCleanData_fish.txt
169650585 ephb4b ZDB-GENE-990415-65 BSPO:0000120 in_left_side_of BFO:0000050 part_of ZFA:0000121 lateral plate mesoderm PATO:0000462 absent abnormal ZDB-FISH-161209-1 TU + MO2-ephb4b ZDB-STAGE-010723-16 ZDB-STAGE-010723-16 ZDB-GENOX-161209-3 ZDB-PUB-160612-7 ZDB-FIG-160818-15
169657538 klf8 ZDB-GENE-070424-152 BSPO:0000120 in_left_side_of BFO:0000050 part_of ZFA:0000101 diencephalon PATO:0000462 absent abnormal ZDB-FISH-180605-11 AB + MO1-klf8 ZDB-STAGE-010723-16 ZDB-STAGE-010723-16 ZDB-GENOX-180605-12 ZDB-PUB-170720-15 ZDB-FIG-180118-30
169657540 klf8 ZDB-GENE-070424-152 BSPO:0000120 in_left_side_of BFO:0000050 part_of ZFA:0000101 diencephalon PATO:0000462 absent abnormal ZDB-FISH-180605-12 AB + MO2-klf8 ZDB-STAGE-010723-16 ZDB-STAGE-010723-16 ZDB-GENOX-180605-13 ZDB-PUB-170720-15 ZDB-FIG-180118-30
169648499 meis3 ZDB-GENE-010406-2 BSPO:0000120 in_left_side_of BFO:0000050 part_of ZFA:0001323 mid intestine PATO:0000462 absent abnormal ZDB-FISH-160212-5 AB + MO1-meis3 ZDB-STAGE-010723-9 ZDB-STAGE-010723-9 ZDB-GENOX-160212-9 ZDB-PUB-150912-13 ZDB-FIG-160212-9
169648501 meis3 ZDB-GENE-010406-2 BSPO:0000120 in_left_side_of BFO:0000050 part_of ZFA:0001076 intestinal bulb PATO:0000628 mislocalised abnormal ZDB-FISH-160212-5 AB + MO1-meis3 ZDB-STAGE-010723-9 ZDB-STAGE-010723-9 ZDB-GENOX-160212-9 ZDB-PUB-150912-13 ZDB-FIG-160212-9
/data $ grep BSPO:0000121 phenoGeneCleanData_fish.txt
169650586 ephb4b ZDB-GENE-990415-65 BSPO:0000121 in_right_side_of BFO:0000050 part_of ZFA:0000121 lateral plate mesoderm PATO:0000628 mislocalised abnormal ZDB-FISH-161209-1 TU + MO2-ephb4b ZDB-STAGE-010723-16 ZDB-STAGE-010723-16 ZDB-GENOX-161209-3 ZDB-PUB-160612-7 ZDB-FIG-160818-15
169648503 meis3 ZDB-GENE-010406-2 BSPO:0000121 in_right_side_of BFO:0000050 part_of ZFA:0001323 mid intestine PATO:0000462 absent abnormal ZDB-FISH-160212-5 AB + MO1-meis3 ZDB-STAGE-010723-9 ZDB-STAGE-010723-9 ZDB-GENOX-160212-9 ZDB-PUB-150912-13 ZDB-FIG-160212-9
169648502 meis3 ZDB-GENE-010406-2 BSPO:0000121 in_right_side_of BFO:0000050 part_of ZFA:0001076 intestinal bulb PATO:0000628 mislocalisedabnormal ZDB-FISH-160212-5 AB + MO1-meis3 ZDB-STAGE-010723-9 ZDB-STAGE-010723-9 ZDB-GENOX-160212-9 ZDB-PUB-150912-13 ZDB-FIG-160212-9
/data $
@matentzn commented on Thu Sep 20 2018
In my latest run, I found a few more of those:
http://purl.obolibrary.org/obo/BSPO_0000120 (in left side of)
http://purl.obolibrary.org/obo/BSPO_0000098 (dorsal to)
http://purl.obolibrary.org/obo/BSPO_0000099 (posterior to)
http://purl.obolibrary.org/obo/BSPO_0000121 (in right side of)
http://purl.obolibrary.org/obo/BSPO_0000096 (anterior to)
Can someone at ZFIN check whether, given, https://zfin.org/downloads/phenoGeneCleanData_fish.txt, Column D, the following replacements can be made to the annotations:
BSPO:0000120 (in left side of) -> BSPO:0000000 (left side)
BSPO:0000098 (dorsal to) -> BSPO: 0000063 (dorsal side)
BSPO:0000099 (posterior to) -> BSPO:0000056 (posterior side)
BSPO:0000121 (in right side of) -> BSPO:0000007 (right side)
BSPO:0000096 (anterior to) -> BSPO:0000055 (anterior side)
... that are not process qualities.
@matentzn commented on Tue Nov 13 2018
The following classes are used across ZP, but are obsoleted/deprecated:
What should happen to the phenotypes? Note that only some of them are in the ZFIN annotations; some are in the current manual intermediate layer.
BSPO_0000101
GO_0000046
GO_0004872
GO_0005578
GO_0005605
GO_0006200
GO_0007067
GO_0008002
GO_0008003
GO_0008105
GO_0015992
GO_0016023
GO_0016265
GO_0016271
GO_0016337
GO_0021865
GO_0021867
GO_0031512
GO_0031513
GO_0040023
GO_0042384
GO_0042516
GO_0043205
GO_0043206
GO_0071436
GO_0072372
GO_0090002
GO_0097369
GO_2001273
GO_2001274
GO_2001275
ZFA_0000283
ZFA_0005182
See also #45
Logical definition:
'has part' some
('increased occurrence' and ('inheres in' some
('protein kinase activity' and ('part of' some 'cardiac ventricle')))
and ('has modifier' some abnormal))
Problem: kinase activity is a process, cardiac ventrical a material entity. part_of is the wrong relation.
Solution: ZFIN record should use 'occurs_in' in column Post-composed Relationship ID
instead of 'part_of'.
Refer to this table to find the broken record.
ZP_0100030 is defined as.
'has part' some
('increased occurrence' and ('inheres in' some
(peritoneum and ('occurs in' some 'macrophage chemotaxis'))) and ('has modifier' some abnormal))
Is it possible that the intention was to record 'macrophage chemotaxis' and ('occurs in' some peritoneum)?
If you agree, review whether this is a general mix up in the ontology (i.e. ALL ZP classes are simply reversed in terms of the 'occurs in' relation), or this is a problem with the ZFIN EQ annotations.
If you find it is a problem with the ZFIN EQs, just fix it in ZFIN, and let me know when the fix is applied and the fish_phenotypes.txt data in the ZFIN downloads sections is updated!
I think fixing that class alone solves about 200 unsatisfiable classes.
Blockers
How did the annotations change?
Which new ZP terms do these relate to?
Which ZP terms are merged/obsoleted?
Yvonne:
- the annotations should really not change
- Exceptions: GO terms change (obsoleted)
- Relationship issues don't really exist anymore
The NBO is planning to retire its Phenotype branch (no date set yet). We are not aware that ZP has been using any terms from this branch, but you may want to double-check. I recommend tagging @matentzn in follow-up comments, not least if you need a technical discussion.
For new term requests, please provide the following information:
yolk edema
combination of yolk in UBERON and edetamous in PATO
not sure
If you would like a nanoattribution, please indicate your ORCID id
The latest release (2019-11-12) is a big improvement over the previous version. When standing alone, all classes are satisfiable. After being incorporated into vertebrate.owl though, some of them became unsatisfied, as listed below:
ZFA_0000435
ZP_0000412
ZP_0002062
ZP_0002510
ZP_0002511
ZP_0002557
ZP_0003019
ZP_0003144
ZP_0003145
ZP_0003428
ZP_0004008
ZP_0004283
ZP_0004284
ZP_0004299
ZP_0005361
ZP_0005362
ZP_0005531
ZP_0005928
ZP_0006699
ZP_0006700
ZP_0006899
ZP_0006921
ZP_0006922
ZP_0008170
ZP_0008184
ZP_0008185
ZP_0008312
ZP_0008768
ZP_0009148
ZP_0010431
ZP_0010686
ZP_0010687
ZP_0010688
ZP_0011448
ZP_0011473
ZP_0011681
ZP_0011709
ZP_0011716
ZP_0011745
ZP_0011889
ZP_0012376
ZP_0012463
ZP_0012500
ZP_0013387
ZP_0014696
ZP_0014741
ZP_0014762
ZP_0014898
ZP_0015602
ZP_0016403
ZP_0016404
ZP_0016405
ZP_0016733
ZP_0016944
ZP_0016945
ZP_0016946
ZP_0017766
ZP_0018215
ZP_0018216
ZP_0018220
ZP_0018289
ZP_0018331
ZP_0019846
ZP_0019851
ZP_0019852
ZP_0019853
ZP_0019854
ZP_0020515
ZP_0020776
ZP_0020778
ZP_0021475
ZP_0021924
ZP_0022946
ZP_0100778
ZP_0100779
ZP_0100967
ZP_0102325
ZP_0102981
ZP_0102982
ZP_0103341
ZP_0103347
ZP_0103558
ZP_0103989
ZP_0106021
ZP_0107100
ZP_0107101
ZP_0108328
We also need to find out how this relates to GO:0001PHENOTYPE classes in dipper.
'cilium multi-ciliated epithelial cell normal, abnormal'
'determination of left/right asymmetry in lateral mesoderm normal, abnormal'
'determination of pancreatic left/right asymmetry normal, abnormal'
'embryonic heart tube left/right pattern formation normal, abnormal'
'trunk normal neural crest cell development, abnormal'
'whole organism normal, abnormal'
Here are the ZFIN annotations I found:
phenotype_fish.txt:ZDB-FISH-150901-10141 WT + MO1-mir34b + MO2-myb ZDB-STAGE-010723-13 Pharyngula:Prim-25 ZDB-STAGE-010723-13 Pharyngula:Prim-25 GO:0005929 cilium BFO:0000050 part_of ZFA:0005242 multi-ciliated epithelial cell PATO:0000461 normal normal ZDB-PUB-130703-10 ZDB-EXP-140205-10
phenotype_fish.txt:ZDB-FISH-150901-12354 eif3ba<sup>la024215Tg/la024215Tg</sup> ZDB-STAGE-010723-10 Pharyngula:Prim-5 ZDB-STAGE-010723-10 Pharyngula:Prim-5 GO:0014032 neural crest cell development BFO:0000066 occurs_in ZFA:0001115 trunk PATO:0000461 normal normal ZDB-PUB-130710-52 ZDB-EXP-041102-1
phenotype_fish.txt:ZDB-FISH-150901-16886 katnb1<sup>mh103/mh103</sup> ZDB-STAGE-010723-2 Gastrula:Shield ZDB-STAGE-010723-2 Gastrula:Shield ZFA:0001094 whole organism PATO:0000461 normal normal ZDB-PUB-141219-3 ZDB-EXP-041102-1
phenotype_fish.txt:ZDB-FISH-150901-19627 kif6<sup>gw326/gw326</sup> ZDB-STAGE-010723-30 Segmentation:14-19 somites ZDB-STAGE-010723-30 Segmentation:14-19 somites GO:0003140 determination of left/right asymmetry in lateral mesoderm PATO:0000461 normal normal ZDB-PUB-141007-7 ZDB-EXP-041102-1
phenotype_fish.txt:ZDB-FISH-150901-19627 kif6<sup>gw326/gw326</sup> ZDB-STAGE-010723-30 Segmentation:14-19 somites ZDB-STAGE-010723-8 Larval:Protruding-mouth GO:0035469 determination of pancreatic left/right asymmetry PATO:0000461 normal normal ZDB-PUB-141007-7 ZDB-EXP-041102-1
phenotype_fish.txt:ZDB-FISH-150901-19627 kif6<sup>gw326/gw326</sup> ZDB-STAGE-010723-32 Pharyngula:Prim-15 ZDB-STAGE-010723-32 Pharyngula:Prim-15 GO:0060971 embryonic heart tube left/right pattern formation PATO:0000461 normal normal ZDB-PUB-141007-7 ZDB-EXP-041102-1
phenotype_fish.txt:ZDB-FISH-150901-3309 katnb1<sup>mh101/mh101</sup>; katnb1<sup>mh102/mh102</sup> ZDB-STAGE-010723-2 Gastrula:Shield ZDB-STAGE-010723-2 Gastrula:Shield ZFA:0001094 whole organism PATO:0000461 normal normal
I thought phenotype fish only contained 'abnormal' now? We need to account for this soon, because we know have abnormally normal phenotypes which looks a bit funny. :P
genus differentia
For new term requests, please provide the following information:
(e.g., Asplenia)
(e.g., Absent spleen)
the definition should be understandable even for non-specialists. Include a PubMed ID to refer to any relevant article that provides additional information about the suggested term.
Please look in the hierarchy in a browser such as OLS
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Lots of duplicates where removed, dont forget to obsolete before next release @matentzn
Analogously to XPO, we would like to have ZFA intermediate classes to make browsing the ZP hierarchy easier. (abnormal morphology, abnormal anatomy)
The OBO Foundry has recently created a topics page at https://github.com/topics/obofoundry. It would be great if you could add the obofoundry
topic to your repository, since it's currently listed as active in the OBO Foundry. If you're not sure how to do that, follow the instructions here. The main issue for this task is at OBOFoundry/OBOFoundry.github.io#1538 in case you want some more context or to join the larger discussion.
@matentzn commented on Wed Sep 12 2018
http://zfin.org/definition/source_information
or
http://zfin/definition/source_information
Should be the former to be valid URL type IRI.
After #32 is closed, we need to add abnormalBiologicalProcess back to external.txt. Currently, abnormalBiologicalProcess uses PATO:quality rather than PATO:process quality to capture all the abnormal biological processes in ZFIN.
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